/*
 *  match: a package to match lists of stars (or other items)
 *  Copyright (C) 2000  Michael William Richmond
 *
 *  Contact: Michael William Richmond
 *           Physics Department
 *           Rochester Institute of Technology
 *           85 Lomb Memorial Drive
 *           Rochester, NY  14623-5603
 *           E-mail: mwrsps@rit.edu
 *
 *
 *  This program is free software; you can redistribute it and/or
 *  modify it under the terms of the GNU General Public License
 *  as published by the Free Software Foundation; either version 2
 *  of the License, or (at your option) any later version.
 *
 *  This program is distributed in the hope that it will be useful,
 *  but WITHOUT ANY WARRANTY; without even the implied warranty of
 *  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
 *  GNU General Public License for more details.
 *
 *  You should have received a copy of the GNU General Public License
 *  along with this program; if not, write to the Free Software
 *  Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA  02111-1307, USA.
 *
 */

/*
 * <AUTO>
 * FILE: match.c
 *
 * <HTML>
 * This file contains the 'main' routine, which takes instructions
 * from the user, reads information from files, calls the matching
 * routines, and writes information back onto disk.
 *
 * </HTML>
 *
 *
 *  7/18/96   - Added transonly option.  MWR
 *
 *  6/1/2000  - Added 'recalc' option; this goes through the usual steps:
 *
 *                     1. read in complete lists of stars from two sources
 *                     2. using only N brightest, find a set of matching pairs
 *                     3. calc TRANS
 *                     4. apply TRANS to all of list A
 *                     5. match all of list A (with TRANS'ed coords) against
 *                              all of list B to find _many_ pairs
 *
 *              but now it also adds the following
 *
 *                     6. using these _many_ pairs, calc TRANS again
 *
 *              The point is to avoid running the similar-triangles code
 *              on the _many_ pairs, since that's the slow part;
 *              we can very quickly calc a new, more accurate TRANS from
 *              the _many_ pairs.
 *
 *              MWR
 *
 * 6/14/2000  - Added "--version" and "--help" options, plus GPL.
 *              MWR
 *
 * 7/30/2000 - Added "id1" and "id2" options.  MWR
 *
 * 1/21/2001 - Added "max_iter" and "halt_sigma" options, plus some sanity
 *             checks on values of user-supplied arguments.
 *             MWR
 *
 * 12/14/2001- Added additional output values in TRANS which describe
 *             the quality of the fit.   Added optional arguments which
 *             cause calculation of additional statistics.
 *             Thanks to John Blakeslee.
 *             MWR
 *
 * 12/31/2001- Added options:
 *                 allow user to specify an input TRANS
 *                 allow user to specify a pure offset between coords
 *             Thanks to John Blakeslee.
 *             MWR
 *
 * 11/23/2002- Fixed bug in "reset_A_coords()" which caused an assert
 *                 failure if given empty lists.  Now the routine
 *                 simply prints a warning message and returns
 *                 with normal code.
 *             MWR
 *
 * 11/4/2011 - Added new options "rotangle=" and "rottol=",
 *                 so that user may specify a range of allowed rotations
 *                 between the two lists of stars.
 *             MWR
 *
 * </AUTO>
 *
 */

#include "core/siril.h"

#include <stdio.h>
#include <stdlib.h>
#include <string.h>
#include <math.h>
#include "gui/utils.h"
#include "algos/PSF.h"
#include "opencv/opencv.h"
#include "registration/matching/misc.h"
#include "registration/matching/match.h"
#include "registration/matching/atpmatch.h"

// #define DEBUG           /* get some of diagnostic output */

static void reset_copy_ids(int numA, struct s_star *star_list_A,
		struct s_star *star_list_A_copy);

static int reset_A_coords(int numA, struct s_star *post_list_A,
		struct s_star *pre_list_A);
static int prepare_to_recalc(int num_matched_A,
		struct s_star *matched_list_A, int num_matched_B,
		struct s_star *matched_list_B, struct s_star *star_list_A_copy,
		TRANS *trans);

// star_match can output either:
// - a Homography matrix (with the right order, set with transformation_type) for linear transformations only (global alignment)
// - a trans matrix (with the right order, set with trans_order) for astrometry solve which can be linear, quadratic or cubic
// The flag for astrometry is used to check whether we are getting the right members to fill:
// if TRUE, we should have a trans_order input and a TRANS* output
// if FALSE, we should have a transformation_type input and a Homography * output
// The function starts by making sure we have the correct inputs/outputs set
int new_star_match(psf_star **s1, psf_star **s2, int n1, int n2, int nobj_override,
		double min_scale, double max_scale, Homography *H, TRANS *t,
		gboolean for_astrometry, transformation_type type, int trans_type,
		s_star **out_list_A, s_star **out_list_B) {
	//sanity checks
	if (for_astrometry) {
		g_assert(t != NULL);
		g_assert(trans_type > AT_TRANS_UNDEFINED);
	} else {
		g_assert(H != NULL);
		g_assert(type >= SHIFT_TRANSFORMATION);
	}
	int numA, numB;
	int num_matched_A, num_matched_B;
	int numA_copy;
	int max_iter = AT_MATCH_MAXITER;
	int trans_order = (for_astrometry) ? trans_type : AT_TRANS_LINEAR; /* for image registration, we will always use linear */
	double triangle_radius = AT_TRIANGLE_RADIUS; /* in triangle-space coords */
	double match_radius = AT_MATCH_RADIUS; /* in units of list B */
	double rot_angle = AT_MATCH_NOANGLE; /* by default, any angle is okay */
	double rot_tol = AT_MATCH_NOANGLE;
	double halt_sigma = AT_MATCH_HALTSIGMA;
	int nobj = AT_MATCH_NBRIGHT;
	int num_matches = 0; /* number of matching pairs */
	struct s_star *star_list_A = NULL, *star_list_B = NULL;
	struct s_star *star_list_A_copy = NULL;
	struct s_star *matched_list_A = NULL, *matched_list_B = NULL;
	TRANS *trans = NULL;
	Homography *Hom = NULL;

	if (min_scale != -1.0 && max_scale != -1.0 && min_scale > max_scale) {
		fprintf(stderr,"min_scale must be smaller than max_scale\n");
		return (SH_GENERIC_ERROR);
	}
#ifdef DEBUG
	if (min_scale == -1.0 && max_scale == -1.0) {
		printf("No limits set on relative scales for matching.\n");
	} else {
		printf("using min_scale %f, max_scale %f\n", min_scale, max_scale);
	}
#endif
	if (nobj_override > 0)
		nobj = min(max(n1, n2), nobj_override);

	/* Check to make sure that the user specified
	 *
	 *       a)   neither "rotangle" nor "rottol"
	 *   or
	 *       b)   both "rotangle" and "rottol"
	 */
	if (rot_angle == AT_MATCH_NOANGLE && rot_tol == AT_MATCH_NOANGLE) {
		/* this is okay */
	} else if (rot_angle != AT_MATCH_NOANGLE
			&& rot_tol != AT_MATCH_NOANGLE) {
		/* this is okay */
	} else {
		/* this is NOT okay */
		fprintf(stderr,"Must specify both 'rotangle' and 'rottol', or neither \n");
		return (SH_GENERIC_ERROR);
	}

	/* we start with an "empty" TRANS; atFindTrans will try to fill it */
	trans = calloc(1, sizeof(TRANS));
	trans->order = trans_order;

#ifdef DEBUG
	printf("using trans_order %d\n", trans_order);
#endif

	/* read information from the first list */
	if (get_stars(s1, n1, &numA, &star_list_A)) {
		shFatal("can't read data\n");
		atTransDel(trans);
		return (SH_GENERIC_ERROR);
	}

	/* We always (whether given initial TRANS or not) will make a second
	 * calculation of the TRANS, using only objects in the set of matched pairs.
	 * As input to this second calculation, we will need items from list A with
	 * their original coordinates.
	 * Therefore, we now create a copy of the stars in set A, so that we can
	 * restore the output matched coords (which have been converted to those in
	 * set B) with the original coords.
	 */
	if (get_stars(s1, n1, &numA_copy, &star_list_A_copy)) {
		atTransDel(trans);
		free_stars(&star_list_A);
		fprintf(stderr,"can't read data\n");
		return (SH_GENERIC_ERROR);
	}

	/* sanity check */
	g_assert(numA_copy == numA);

	/* reset the 'id' field values in the star_list_A_copy so that they
	 * match the 'id' field values in their counterparts in star_list_A
	 */
	reset_copy_ids(numA, star_list_A, star_list_A_copy);

	/* read information from the second list */
	if (get_stars(s2, n2, &numB, &star_list_B)) {
		atTransDel(trans);
		free_stars(&star_list_A);
		free_stars(&star_list_A_copy);
		printf("can't read data\n");
		return (SH_GENERIC_ERROR);
	}

	/* Now, as the has not given us an initial TRANS structure, we need
	 * to find one ourselves.
	 */
	int ret = atFindTrans(numA, star_list_A, numB, star_list_B, triangle_radius,
			nobj, min_scale, max_scale, rot_angle, rot_tol, max_iter,
			halt_sigma, trans);
	if (ret != SH_SUCCESS) {
#ifdef DEBUG
		fprintf(stderr, "initial call to atFindTrans failed\n");
#endif
		/** */
		atTransDel(trans);
		free_stars(&star_list_A);
		free_stars(&star_list_A_copy);
		free_stars(&star_list_B);
		/** */
		return (SH_GENERIC_ERROR);
	}

#ifdef DEBUG
	printf("using trans_order %d.\n", trans_order);
	printf("Initial trans structure:\n");
	print_trans(trans);
#endif

	/* having found (or been given) the TRANS that takes A -> B, let us apply
	 * it to all the elements in A; thus, we'll have two sets of
	 * of stars, each in the same coordinate system
	 */
	atApplyTrans(numA, star_list_A, trans);

	/* now match up the two sets of items, and find four subsets:
	 *
	 *     those from list A that do     have matches in list B
	 *     those from list B that do     have matches in list A
	 *     those from list A that do NOT have matches in list B
	 *     those from list B that do NOT have matches in list A
	 *
	 * We may use the two sets of matched objects for further processing,
	 * so we put the names of the files containing those matched objects
	 * into 'matched_file_A' and 'matched_file_B' for easy reference.
	 */
	atMatchLists(numA, star_list_A, numB, star_list_B, match_radius, &num_matches, &matched_list_A, &matched_list_B);
	trans->nm = num_matches;
	num_matched_B = num_matched_A = num_matches;

	/* The user didn't give us any information about an initial TRANS, so we
	 * called 'atFindTrans()' to find one.
	 * We have applied this TRANS to input list A, and looked for matched pairs.
	 *
	 * Now, we want to improve the initial TRANS, whether it was supplied
	 * by user or determined by 'atFindTrans()'.  We do so by applying
	 * the initial TRANS to only the matched objects in list A, and then
	 * calling 'atRecalcTrans()' on the matched objects only.  This should
	 * give an improved TRANS, since it very likely won't be contaminated
	 * by any spurious matches.
	 */

	/* need to send trans to prepare_to_recalc because it adds sdx,sdy to it */
	if (prepare_to_recalc(num_matched_A, matched_list_A,
			num_matched_B, matched_list_B, star_list_A_copy, trans) != 0) {
		fprintf(stderr,"prepare_to_recalc fails\n");
		/** */
		atTransDel(trans);
		free_stars(&matched_list_A);
		free_stars(&matched_list_B);
		free_stars(&star_list_A);
		free_stars(&star_list_B);
		free_stars(&star_list_A_copy);
		/** */
		return (SH_GENERIC_ERROR);
	}
	/* okay, now we're ready to call atRecalcTrans, on matched items only */
	if (atRecalcTrans(num_matched_A, matched_list_A, num_matched_B,
			matched_list_B, max_iter, halt_sigma, trans) != SH_SUCCESS) {
#ifdef DEBUG
		fprintf(stderr,"atRecalcTrans fails on matched pairs only\n");
#endif
		/** */
		atTransDel(trans);
		free_stars(&matched_list_A);
		free_stars(&matched_list_B);
		free_stars(&star_list_A);
		free_stars(&star_list_B);
		free_stars(&star_list_A_copy);
		/** */
		return (SH_GENERIC_ERROR);
	}
#ifdef DEBUG
	printf("TRANS based on matches only :\n");
	print_trans(trans);
#endif

	/* At this point, we have a TRANS which is based solely on those items
	 * which matched.  If the user wishes, we can improve the TRANS
	 * even more by applying the current transformation to ALL items
	 * in list A, making a second round of matching pairs, and then
	 * using these pairs to calculate a new and better TRANS.
	 *
	 * The point is that we'll probably end up with more matched pairs
	 * if we start with the current TRANS, instead of the initial TRANS.
	 */

	/* re-set coords of all items in star A */
	if (reset_A_coords(numA, star_list_A, star_list_A_copy) != 0) {
		shFatal("reset_A_coords returns with error before recalc");
	}

	/* apply the current TRANS (which is probably much better than
	 * the initial TRANS) to all items in list A
	 */
	atApplyTrans(numA, star_list_A, trans);

	/* Match items in list A to those in list B */
	free_stars(&matched_list_A);
	free_stars(&matched_list_B);
	atMatchLists(numA, star_list_A, numB, star_list_B, match_radius, &num_matches, &matched_list_A, &matched_list_B); // causes memleak

	trans->nm = num_matches;
	num_matched_B = num_matched_A = num_matches;
#ifdef DEBUG
	printf("After tuning with recalc, num matches is %d\n", num_matches);
	print_trans(trans);
#endif

	/* prepare to call atRecalcTrans one last time */
	/* need to send trans to prepare_to_recalc because it adds sdx,sdy */
	if (prepare_to_recalc(num_matched_A, matched_list_A,
			num_matched_B, matched_list_B, star_list_A_copy, trans) != 0) {
		fprintf(stderr,"prepare_to_recalc fails\n");
		/** */
		atTransDel(trans);
		free_stars(&matched_list_A);
		free_stars(&matched_list_B);
		free_stars(&star_list_A);
		free_stars(&star_list_B);
		free_stars(&star_list_A_copy);
		/** */
		return (SH_GENERIC_ERROR);
	}

	/* final call atRecalcTrans, on matched items only */
	if (atRecalcTrans(num_matched_A, matched_list_A, num_matched_B,
			matched_list_B, max_iter, halt_sigma, trans) != SH_SUCCESS) {
#ifdef DEBUG
		fprintf(stderr,"atRecalcTrans fails on matched pairs only\n");
#endif
		/** */
		atTransDel(trans);
		free_stars(&matched_list_A);
		free_stars(&matched_list_B);
		free_stars(&star_list_A);
		free_stars(&star_list_B);
		free_stars(&star_list_A_copy);
		/** */
		return (SH_GENERIC_ERROR);
	}

#ifdef DEBUG
	printf("TRANS based on recalculated matches is \n");
	print_trans(trans);
#endif
	if (!for_astrometry) { // we will compute the full linear up to HOMOGRAPHY_TRANSFORMATION with opencv
		Hom = atHNew();
		Hom->pair_matched = num_matches;

		if (atPrepareHomography(num_matched_A, matched_list_A, num_matched_B,
				matched_list_B, Hom, for_astrometry, type)) {
			fprintf(stderr, "atPrepareHomography failed to compute H\n");
			/** */
			atTransDel(trans);
			atHDel(Hom);
			free_stars(&matched_list_A);
			free_stars(&matched_list_B);
			free_stars(&star_list_A);
			free_stars(&star_list_B);
			free_stars(&star_list_A_copy);
			/** */
			return (SH_GENERIC_ERROR);
		}
#ifdef DEBUG
		print_H(Hom);
#endif
		*H = *Hom;
	} else {
		*t = *trans;
	}

	if (out_list_A)
		*out_list_A = matched_list_A;
	else free_stars(&matched_list_A);
	if (out_list_B)
		*out_list_B = matched_list_B;
	else free_stars(&matched_list_B);

	/* clean up memory */
	atTransDel(trans);
	atHDel(Hom);
	free_stars(&star_list_A);
	free_stars(&star_list_B);
	free_stars(&star_list_A_copy);

	return 0;
}

// star_match can output either:
// - a Homography matrix (with the right order, set with transformation_type) for linear transformations only (global alignment)
// - a trans matrix (with the right order, set with trans_order) for astrometry solve which can be linear, quadratic or cubic
// The flag for astrometry is used to check whether we are getting the right members to fill:
// if TRUE, we should have a trans_order input and a TRANS* output
// if FALSE, we should have a transformation_type input and a Homography * output
// The function starts by making sure we have the correct inputs/outputs set
int re_star_match(psf_star **s1, psf_star **s2, int n1, int n2,
		TRANS *trans, s_star **out_list_A, s_star **out_list_B) {
	//sanity checks

	int numA, numB;
	int num_matched_A, num_matched_B;
	int numA_copy;
	int max_iter = AT_MATCH_MAXITER;
	double match_radius = AT_MATCH_RADIUS; /* in units of list B */
	double halt_sigma = AT_MATCH_HALTSIGMA;
	int num_matches = 0; /* number of matching pairs */
	struct s_star *star_list_A = NULL, *star_list_B = NULL;
	struct s_star *star_list_A_copy = NULL;
	struct s_star *matched_list_A = NULL, *matched_list_B = NULL;

#ifdef DEBUG
	printf("using trans_order %d\n", trans_order);
#endif

	/* read information from the first list */
	if (get_stars(s1, n1, &numA, &star_list_A)) {
		shFatal("can't read data\n");
		return (SH_GENERIC_ERROR);
	}

	/* We always (whether given initial TRANS or not) will make a second
	 * calculation of the TRANS, using only objects in the set of matched pairs.
	 * As input to this second calculation, we will need items from list A with
	 * their original coordinates.
	 * Therefore, we now create a copy of the stars in set A, so that we can
	 * restore the output matched coords (which have been converted to those in
	 * set B) with the original coords.
	 */
	if (get_stars(s1, n1, &numA_copy, &star_list_A_copy)) {
		free_stars(&star_list_A);
		fprintf(stderr,"can't read data\n");
		return (SH_GENERIC_ERROR);
	}

	/* sanity check */
	g_assert(numA_copy == numA);

	/* reset the 'id' field values in the star_list_A_copy so that they
	 * match the 'id' field values in their counterparts in star_list_A
	 */
	reset_copy_ids(numA, star_list_A, star_list_A_copy);

	/* read information from the second list */
	if (get_stars(s2, n2, &numB, &star_list_B)) {
		free_stars(&star_list_A);
		free_stars(&star_list_A_copy);
		printf("can't read data\n");
		return (SH_GENERIC_ERROR);
	}


#ifdef DEBUG
	printf("using trans_order %d.\n", trans_order);
	printf("Initial trans structure:\n");
	print_trans(trans);
#endif

	/* having found (or been given) the TRANS that takes A -> B, let us apply
	 * it to all the elements in A; thus, we'll have two sets of
	 * of stars, each in the same coordinate system
	 */
	atApplyTrans(numA, star_list_A, trans);

	/* now match up the two sets of items, and find four subsets:
	 *
	 *     those from list A that do     have matches in list B
	 *     those from list B that do     have matches in list A
	 *     those from list A that do NOT have matches in list B
	 *     those from list B that do NOT have matches in list A
	 *
	 * We may use the two sets of matched objects for further processing,
	 * so we put the names of the files containing those matched objects
	 * into 'matched_file_A' and 'matched_file_B' for easy reference.
	 */
	atMatchLists(numA, star_list_A, numB, star_list_B, match_radius, &num_matches, &matched_list_A, &matched_list_B);
	trans->nm = num_matches;
	num_matched_B = num_matched_A = num_matches;

	/* The user didn't give us any information about an initial TRANS, so we
	 * called 'atFindTrans()' to find one.
	 * We have applied this TRANS to input list A, and looked for matched pairs.
	 *
	 * Now, we want to improve the initial TRANS, whether it was supplied
	 * by user or determined by 'atFindTrans()'.  We do so by applying
	 * the initial TRANS to only the matched objects in list A, and then
	 * calling 'atRecalcTrans()' on the matched objects only.  This should
	 * give an improved TRANS, since it very likely won't be contaminated
	 * by any spurious matches.
	 */

	/* need to send trans to prepare_to_recalc because it adds sdx,sdy to it */
	if (prepare_to_recalc(num_matched_A, matched_list_A,
			num_matched_B, matched_list_B, star_list_A_copy, trans) != 0) {
		fprintf(stderr,"prepare_to_recalc fails\n");
		/** */
		free_stars(&matched_list_A);
		free_stars(&matched_list_B);
		free_stars(&star_list_A);
		free_stars(&star_list_B);
		free_stars(&star_list_A_copy);
		/** */
		return (SH_GENERIC_ERROR);
	}
	/* okay, now we're ready to call atRecalcTrans, on matched items only */
	if (atRecalcTrans(num_matched_A, matched_list_A, num_matched_B,
			matched_list_B, max_iter, halt_sigma, trans) != SH_SUCCESS) {
#ifdef DEBUG
		fprintf(stderr,"atRecalcTrans fails on matched pairs only\n");
#endif
		/** */
		free_stars(&matched_list_A);
		free_stars(&matched_list_B);
		free_stars(&star_list_A);
		free_stars(&star_list_B);
		free_stars(&star_list_A_copy);
		/** */
		return (SH_GENERIC_ERROR);
	}
#ifdef DEBUG
	printf("TRANS based on matches only :\n");
	print_trans(trans);
#endif

	/* At this point, we have a TRANS which is based solely on those items
	 * which matched.  If the user wishes, we can improve the TRANS
	 * even more by applying the current transformation to ALL items
	 * in list A, making a second round of matching pairs, and then
	 * using these pairs to calculate a new and better TRANS.
	 *
	 * The point is that we'll probably end up with more matched pairs
	 * if we start with the current TRANS, instead of the initial TRANS.
	 */

	/* re-set coords of all items in star A */
	if (reset_A_coords(numA, star_list_A, star_list_A_copy) != 0) {
		shFatal("reset_A_coords returns with error before recalc");
	}

	/* apply the current TRANS (which is probably much better than
	 * the initial TRANS) to all items in list A
	 */
	atApplyTrans(numA, star_list_A, trans);

	/* Match items in list A to those in list B */
	free_stars(&matched_list_A);
	free_stars(&matched_list_B);
	atMatchLists(numA, star_list_A, numB, star_list_B, match_radius, &num_matches, &matched_list_A, &matched_list_B); // causes memleak

	trans->nm = num_matches;
	num_matched_B = num_matched_A = num_matches;
#ifdef DEBUG
	printf("After tuning with recalc, num matches is %d\n", num_matches);
	print_trans(trans);
#endif

	/* prepare to call atRecalcTrans one last time */
	/* need to send trans to prepare_to_recalc because it adds sdx,sdy */
	if (prepare_to_recalc(num_matched_A, matched_list_A,
			num_matched_B, matched_list_B, star_list_A_copy, trans) != 0) {
		fprintf(stderr,"prepare_to_recalc fails\n");
		/** */
		free_stars(&matched_list_A);
		free_stars(&matched_list_B);
		free_stars(&star_list_A);
		free_stars(&star_list_B);
		free_stars(&star_list_A_copy);
		/** */
		return (SH_GENERIC_ERROR);
	}

	/* final call atRecalcTrans, on matched items only */
	if (atRecalcTrans(num_matched_A, matched_list_A, num_matched_B,
			matched_list_B, max_iter, halt_sigma, trans) != SH_SUCCESS) {
#ifdef DEBUG
		fprintf(stderr,"atRecalcTrans fails on matched pairs only\n");
#endif
		/** */
		free_stars(&matched_list_A);
		free_stars(&matched_list_B);
		free_stars(&star_list_A);
		free_stars(&star_list_B);
		free_stars(&star_list_A_copy);
		/** */
		return (SH_GENERIC_ERROR);
	}

#ifdef DEBUG
	printf("TRANS based on recalculated matches is \n");
	print_trans(trans);
#endif


	if (out_list_A)
		*out_list_A = matched_list_A;
	else free_stars(&matched_list_A);
	if (out_list_B)
		*out_list_B = matched_list_B;
	else free_stars(&matched_list_B);

	/* clean up memory */
	free_stars(&star_list_A);
	free_stars(&star_list_B);
	free_stars(&star_list_A_copy);

	return 0;
}

/***********************************************************************
 * FUNCTION: reset_copy_ids
 *
 * Modify the 'id' field values in the given list (a copy of list A)
 *   so that they will match the 'id' values in the corresponding
 *   stars of list A.
 *
 * We have to do this because the routine which creates new s_star
 *   structs keeps incrementing the 'id' values, and so the copies
 *   have a different value.
 *
 * RETURNS
 *   nothing
 */

static void reset_copy_ids(int numA, /* I: number of stars in list A */
struct s_star *star_list_A, /* I: original star A list */
struct s_star *star_list_A_copy /* I/O: copy of star A list */
) {
	int i;
	struct s_star *star, *star_copy;

	star = star_list_A;
	star_copy = star_list_A_copy;
	for (i = 0; i < numA; i++) {
		g_assert(star != NULL);
		g_assert(star_copy != NULL);
		star_copy->id = star->id;

		star = star->next;
		star_copy = star_copy->next;
	}
}

/***********************************************************************
 * FUNCTION: reset_A_coords
 *
 * Given the number of elements in list 'post_list_A',
 *   and two versions of the
 *   stars in list A (after conversion to coord system of list B,
 *   and before conversion), restore the original coords of stars
 *   in the the matched list.
 *
 * RETURNS
 *   0            if all goes well
 *   1            otherwise
 */

static int reset_A_coords(int numA, /* I: number of stars in the list */
struct s_star *post_list_A, /* I/O: stars in A, after they have */
/*         been matched to stars in  */
/*         list B; coords have been */
/*         converted.  We'll reset  */
/*         coords in this list */
struct s_star *pre_list_A /* I: stars in A, with original coords */
) {
	int post_index;
	struct s_star *pre_star, *post_star;

	/* if handed empty list, do nothing. */
	if (numA == 0) {
		shError("reset_A_coords: handed empty list, will do nothing");
		return (0);
	}

	/* sanity checks */
	g_assert(post_list_A != NULL);
	g_assert(pre_list_A != NULL);

	for (post_index = 0, post_star = post_list_A; post_index < numA;
			post_index++, post_star = post_star->next) {

		g_assert(post_star != NULL);

		int found_it = 0;
		pre_star = pre_list_A;
		while (pre_star != NULL) {

			if (pre_star->id == post_star->id) {
				post_star->x = pre_star->x;
				post_star->y = pre_star->y;
				found_it = 1;
				break;
			}
			pre_star = pre_star->next;
		}
		if (found_it == 0) {
			printf("reset_A_coords: no match for post_star %d?\n", post_index);
			return 1;
		}
	}

	return 0;
}

/**********************************************************************
 * PROCEDURE: prepare_to_recalc
 *
 * DESCRIPTION: This function sets us up to call "atRecalcTrans".
 *              We have already found (or been given) a TRANS, and
 *              used it to match up items from list A and list B.
 *              Those matched items are in a pair of files
 *              with names based on 'outfile', but with
 *              extensions "mtA" and "mtB".
 *              Ex: if 'outfile' is "matched",
 *              then the two sets of matched items are in
 *
 *                    matched.mtA      matched.mtB
 *
 *              The format of each file is one star per line,
 *              with 4 fields:
 *
 *                    internal_ID     xval   yval     mag
 *
 *              where the coords (xval, yval) are in system of list B.
 *
 *              We are about to use these good, matched items to
 *              find an improved TRANS -- which should take objects
 *              from coord system A to coord system B.
 *
 *              In order to do that, we need to
 *
 *                  a. Read in the good, matched items.  The coordinates
 *                     of objects in list A will have been transformed
 *                     to their corresponding values in coord system
 *                     of list B, so ...
 *
 *                  b. We must then re-set the coords of the items in
 *                     list A to their original values, so that we can
 *                     re-calculate a TRANS which takes the coords
 *                     from system A to system B.
 *
 *              We also take this opportunity to compare the transformed
 *              positions of items in list A against the positions of
 *              the matching objects in list B.  We calculate the
 *              RMS of the differences in both "x" and "y" directions,
 *              and place them into the "sx" and "sy" members of
 *              the current TRANS.
 *
 *
 * RETURNS:
 *    0             if all goes well
 *    1             if there's an error
 */

static int prepare_to_recalc(int num_matched_A, /* O: number of stars in matched set */
/*      from list A */
struct s_star *matched_list_A, /* O: fill this with matched items from */
/*      list A, in coord system B */
int num_matched_B, /* O: number of stars in matched set */
/*      from list B */
struct s_star *matched_list_B, /* O: fill this with matched items from */
/*      list B, in coord system B */
struct s_star *star_list_A_copy, /* O: fill this with matched items from */
/*      list A, with their orig coords  */
TRANS *trans /* O: we calc herein the sx, sy fields  */
/*      so put them into this TRANS */
) {
	double Xrms, Yrms;

	/* here we find the rms of those stars we read in -- JPB 17/Jan/02 */
	if (atCalcRMS(num_matched_A, matched_list_A, num_matched_B,
			matched_list_B, &Xrms, &Yrms) != SH_SUCCESS) {
		fprintf(stderr,"atCalcRMS fails on matched pairs\n");
	}
	trans->sx = Xrms;
	trans->sy = Yrms;
	/************************************************/
	if (reset_A_coords(num_matched_A, matched_list_A, star_list_A_copy)
			!= 0) {
		shError("prepare_to_recalc: reset_A_coords returns with error");
		return (1);
	}

	return (0);
}
